Generational Science
by User724
Summary: Sophie Newell has always known her parents were a bit odd. But when she finds a mysterious metal cube in her mother's closet, she'll find out that's odd with a capital Portal.
1. Prolouge

_**Yeah, this is the same story I just posted a teaser for. I've decided to go on with it myself, but ideas are welcome.**_

" _And so the Knight and his Lady shared their first kiss, and they lived happily ever after. The end"*_

"Nice story."

Wheatley turned around, startled by Chell's quiet entrance. "Oh, I-I hope you don't mind, the only story I know is, well, _ours._ But-but don't worry, I kid-proofed it. Replaced _Her_ with an evil queen, made the Portal Gun a magic bow-It's not enough is it? Can't sugarcoat a story like that, it's definitely not G-rated, or whatever it is for toddlers. I've probably scarred Sophie for life now haven't I-?"

"Wheatley, I liked it."

" _Oh._ well, thank you. It's just that…" Wheatley's eyes drifted over to the closet, where the infamous Companion Cube was hidden. "Are you sure we can pull this off? We're not exactly the picture perfect family. And with our rotten luck, she'll probably find me out on her fourth birthday."

"Well then maybe it's time we made our own luck."

Chell pulled him into a kiss, and his brain short-circuited. But as they went to bed, Wheatley wondered how long they could keep their past hidden.

" _Just a few more years,"_ he prayed, _"that's all I ask…"^_

 ***If it's not obvious, Wheatley's bedtime story is "The Heart of the Exile" by elvenwhovian. I haven't read it, but I looked up the ending for this.**

 **^This line was stolen from the Tennis Shoes Adventure Series, but I can't remember which book.**


	2. The Journal

The Diary of Sophie Newell

April 12 ?

 _My parents are insane._

 _Now I know every teenager says that about their parents, but other parents don't wake up in the middle of the night screaming "grab me", other parents don't stare at the full moon like they almost lost someone up there,_ other _parents don't freak out if I go too far Northeast!_

 _I'm getting ahead of myself, my name is Sophie Newell. I am fourteen years old, and I live in a little town called Eaden. I tend to ramble a little (like I'm doing now), but I am NOT dumb and neither is my dad, anyone who feels different can talk to my fists._

 _But back to my parents, they've acting weird for as long as I can remember. Back when I was four, my dad used to tell me a bedtime story about a girl with a magic bow. When I asked if I could have a bow like that, dad told me that the story wasn't true, that magic didn't exist, and that if any of that was real, the characters would probably have PTSD. If I think back, I can still remember the exact moment my imagination died._

 _Then, when I was six, I asked them how they met, and they spent a solid minute staring at each other before dad babbled something about meeting at work (dad is a terrible liar)._

 _So yeah, those things are weird, but the weirdest thing about my parents is how_ content _they are. Eaden is literally a dead end town, but they have no intention of ever leaving, and they don't want me to either. Lucky for them, we don't have nearly enough money for me to go to medical school. But a girl can dream, right?_

Sophie sighed as she put her journal back in the hole behind her Gordon Freeman poster. "Another day, another pointless walk through town."

" _Ellie is so lucky,"_ Sophie thought bitterly. Ellie Otten, age 19, had been her best friend/surrogate sister "since forever," but ever since she had announced that she was moving to New Detroit for college, Sophie couldn't help but feel jealous.

"Hey Sophie!"

Almost as if she knew Sophie had been thinking about her, Ellie came down the road and gave Sophie a hug "I'm gonna miss you."

"I'm going to miss you too." Sophie said, "Congrats on the scholarship!"

"Thanks! I'm so lucky I got in."

" _I know."_ Sophie wanted to say, but instead she said "Nah, you're a natural! I just wish I had that kind of excitement in my life."

That's when Ellie saw it. As Sophie expressed her wish for adventure, her cool blue eyes seemed to flare brighter- _electrically_ brighter.

Ellie blinked, and Sophie's eyes were back to normal. "Uh…you'll get there eventually. Don't give up!"

As Sophie walked away, Ellie tried to forget her vision. But those _eyes._ " _Just like in my nightmare…"_

—

 _Ellie ran through a dark corridor, trying to ignore the little blue lights signifying the walls could shift at any moment. "Come on Sophie, we're almost there!"_

" _ **Oh, you're not going anywhere…"**_ _Said a terrifying, cold mechanical voice._ _ **"Not until you learn the truth."**_

 _With that, laughter rang through the air, maniacal and insane and terrifyingly_ familiar. _Ellie turned to see Sophie staring openmouthed at a screen, eyes glowing bright blue._

" _Actually," said the voice from the screen, "why do we have to leave right_ now _?"_

—

Ellie woke with a scream. She'd been having these dreams for 3 nights now, seeing herself and Sophie trapped in some awful metal labyrinth. Sometimes Sophie would be injured by something, other times she would become sidetracked by that gigantic… _thing_ with Wheatley's voice. But in every one of those dreams, Sophie had glowing blue eyes.


	3. The Cube

Wheatley was overwhelmed.

For starters, he was rubbish at math, in fact he was pretty sure one of the reasons he was chosen to be the Intelligence Dampening Sphere was his complete inability to understand anything numerical. And yet _he_ was the one doing the bills.

Wheatley sighed as he checked his answer for the 78 & 1/2th time in five minutes. He was no expert, but he was pretty sure they couldn't afford to send Sophie to _high_ school, let alone med school like she always wanted. And if their financial trouble wasn't enough, the Cube was acting up again.

Chell had kept the metal box to remind herself of how lucky she was, but for reasons they didn't particularly want to understand, the Companion Cube always started playing music in the week leading up to the anniversary of Chell's escape. Maybe it was GLaDOS' sick idea of a joke. But the point was, it was dangerous. If Sophie found it, and it somehow led her back to Aperture, he could never forgive himself. (There was also the whole thing with Sophie learning about his past and hating him for the rest of forever, but that wasn't important.)

Wheatley wished he could help, he really did. But short of selling the Companion Cube or the Long Fall Boots (bad idea), there was nothing he could do. He just hoped Sophie didn't resent him for this.

Unfortunately, Wheatley was so absorbed in his thoughts, he forgot to hide the Cube in the basement.

—

 _Later_

The moon was almost full, but no one noticed thanks to a massive rainstorm (Earth's climate was still recovering from the Combine's terraforming, so random storms like this happened occasionally. But hey, at least it wasn't _acid_ rain). In fact, this rainstorm was _so_ massive, Sophie's bedroom ceiling had developed a leak. Hence why she was currently in a sleeping bag in her parent's room, having just been startled awake by a clap of thunder.

Sophie was just about to go back to sleep when she heard a strange noise coming from a few feet to her right. Wait, that wasn't noise, that was _music._ Why was there music coming from her mother's closet?

Carefully, Sophie crept out of her sleeping bag, walked to the closet, and slowly opened the door.

After shifting a few boxes, she found the source of the sound, a metal cube about 1 1/2 feet in diameter.

" _What is this thing, a safe? What have my parents got to hide?"_ Sophie knew she shouldn't be snooping in her parent's closet, but as much as she was her mother's child, she sometimes displayed traits from Wheatley, and one of those traits was stupid curiosity.

As Sophie attempted to pry the top off of the strange box, she heard a faint *click* and the music abruptly stopped. Then, hearing her father muttering something about piano lessons, she quickly put the cube back in it's hiding place, closed the closet door, and darted back into bed.

The Companion Cube no longer made any audible sound, but had Wheatley still been a robot, he would have heard the shrill, dog-whistle like sound of a homing beacon.


	4. The Blip

Mike Morasky, 2 1/2 year employee of Pluot Electronic Technologies Incorporated, spent that stormy night the same way he did every night: watching a screen.

It hadn't always been like this. Back when he'd first joined up, armed with a Master's Degree in computer science from Freeman University, he'd been honored to work at Pluot. But three months in, he'd been transferred to the boss' pet project: Aperture.

Johnathan Coulton was the sole reason for Pluot's success, he had bought the struggling startup and singlehandedly transformed it into the leading tech giant it was today in just 14 years! The world knew him as a visionary and a genius businessman, but inside his company he was most famous for his obsession with the defunct facility.

Mike didn't understand it. No one in living memory knew where Aperture was, and after decades of neglect, the place was surely scrap metal, yet here he was, still watching this screen.

"Hey Mike, my shift yet?"

"Yeah." Mike said as his coworker, Geoff Keighley walked in. "You know, sometimes I'm just tempted to smash this stupid thing and be done with it."

"I know, right? But then we'd lose "years of research.""

Mike chuckled at the memory. Back when he and Geoff were first assigned to this project, their manager, Erik Wolepaw, had informed them that this dingy radar was attached to the most powerful satellite array in Michigan, and calibrated to some arbitrary parameters he'd pulled from a massive antenna hijack 14 years ago. Everyone else knew it was just some kid trying to cause a panic, but Erik insisted it matched up with some classified document he'd dug up, and that it just _had_ to have something to do with Aperture.

Mike sighed in annoyance. He could have stayed in school and gotten his PHD, but instead he was wasting his life _watching this screen._ "Hey Mike?"

Mike turned around at the door, he figured Geoff was going to ask for a quarter, or a not-really-5-minute bathroom break. After 2.5 years of nothing, he was totally unprepared for what Geoff said next:

"We got a blip."

* * *

Five minutes later, everyone involved with the project was buzzing around like antlions, trying to trace the signal.

"Got it!" said Kim Swift, a recent transfer from Faucet Tech. "Whatever it is, it's contacted a secure server somewhere upstate. How are any of their computers still _working?_ "

"I have no idea," said Chet Falizek "but I can't seem to hack it. The system is _learning_ from my every attack!"

"Oh," said Erik, just walking into the room, "its _H_ _er_."

 _She_ was Aperture's biggest project, and also it's last. The day She was activated was the day all of Aperture's employees disappeared, and the day the facility was locked down forever. Of course, no machine could be truly sentient, but this thing was supposedly pretty darn close. One thing was for certain: if GLaDOS was still active, there was no way they could ever hack Her.

"Its no use," Erik told the boss over his pager. "Someone will have to go there and shut Her down from the inside."

"It's not a _her_ ," Johnathan replied sharply, "it's a computer."

"A very powerful supercomputer in complete control of the entire Enrichment Center." Erik shot back, "We can't hack her from the outside."

"What if they don't make it?" The boss asked, "If the world finds out we got our employees killed, we'll be ruined!"

"Uh..."

"Wait, where did the homing signal come from?"

"Oh! Uh, a little town called Eaden."


	5. The Call

April 18, ?

"How do you do it? The not-talking? I mean, I can barely shut up for five minutes, but you didn't say a word for..however long that was...It's not important. What _is_ important is your superhuman ability to stay quiet! Did you go to some school, maybe train under a sect of silent... nuns or something? Ugh, never mind. Here's your five dollars."

Sophie came down from her room, not knowing or caring what insane bet her father had made this time. It had been almost a week since the incident with the cube, and Sophie had concluded that it was some sort of music box, or one of Garret's inventions, and had decided to leave it alone.

At least, until two nights ago.

"Hello?" Sophie blinked the exhaustion out of her eyes. Her parents were already asleep, and she wasn't far behind. " _Who in their right mind would call at 11:00?_

 **"Hello Sophie."**

"What? How do you know my name?"

 **"We know a lot of things miss Newell, although it did take us a while to find you. Thanks for turning on that cube."**

"How did you-?"

 **"That's not important. Look, the cube came from an abandoned underground facility Northeast of your hometown, a facility we are very... interested in"**

Sophie's heart skipped a beat, _t_ _he Northeast?_ Her parents were overprotective in general, but they had always specifically warned her never to go Northeast. Now she knew why. "Why me?" She asked skeptically, "And what do I get out of this?"

 **"We can't go in ourselves, too high profile. But you're just a kid, the ...security systems won't notice you. As for payment, we have the** **resources to get you into med school."**

Sophie thought for a moment. This whole thing seemed ridiculous, but it explained her parent's odd behavior. This guy still seemed fishy though. "What kind of security systems?"

 **"Something's been blocking our hacking attempts, but I'm sure it's just another computer. We'll provide you a way to shut it down. Are you in?**

"I'll...consider it." Sophie said, though she wasn't really considering it at all. Money or no money, you don't accept jobs from guys on the phone.

 **"Good. To contact me, dial 1-800-PLUOT and ask for the advisor."**

The phone clicked as the mystery man hung up, leaving Sophie to wonder what the heck just happened.


	6. The Talk

Sophie shook herself out of the memory and pondered what to do for the billionth time. As suspicious as it was, the offer was tempting, and how dangerous could an abandoned laboratory be? Plus, there was the more pressing issue of how this guy found her family, and Sophie had a sick feeling it was her fault.

 _"There's no other choice,"_ Sophie decided, _"I'll have to go to mom and dad."_

Wheatley was no expert, but he was pretty sure that when your teenager _wanted_ to talk to you, it was pretty special. So he was actually looking forward to this little chat with Sophie...until she brought out the Cube.

"So, I found this in the closet the night of the storm. It set off some sort of homing signal, and two nights ago this guy called me asking me to-"

" _What?!_ He wanted you to go _Northeast?!_ Sophie, you can't ever, _ever_ go-"

"Go _where_ dad? Enough dodging, _what is to the Northeast?_ "

Wheatley wasn't the best at nonverbal communication, but the look he gave Chell then was crystal clear: _Your turn._

"It's an underground research facility." Chell began, "There are no humans left, but the machines are very active and _very_ dangerous. Your father and I... We barely escaped alive."

Sophie couldn't believe her ears. First there was an abandoned lab outside of town, and now her parents had been there? "No. no way, this isn't possible!"

"Why do you think we stayed here sweetie?" Wheatley stepped up to help. " _She_ tracked us here. If anything happens to the others because of that..."

Sophie probably should have asked who "She" was, but right now she was too mad to care. "You mean that's why we're stuck here? That's why you don't have a real job? _That's_ why I can't go to school? Because you're "protecting" the town from some underground scrap heap?!"

Wheatley was caught off guard by the outburst. "Sophie, it's not-"

"That was fourteen years ago, there's nothing down there!"

"Honey please, just promise me you won't go there."

"Even if anything _was_ working, how could _you_ protect anyone?"

" _Promise me._ "

"I hate you!" Sophie ran upstairs and slammed the door to her room. She barely managed to call the Pluot guy and tell him the bad news before she collapsed on the bed and cried herself to sleep.


	7. The Ultimatum

"No?! What do you mean no?!"

Back at Pluot headquarters, Johnathan Coulton was _not_ happy.

"My parents found out about you, there's no way I'll be able to sneak out now. I'm sorry."

Johnathan forced himself to remain calm. "That's alright Miss Newell, we'll think of something else. I'm sorry you couldn't make it."

As soon as Sophie hung up, Johnathan paged Erik. "Where does she live?"

"What does it matter sir?" Erick asked. "She said she couldn't come-"

"Because of her parents." Johnathan cut in, his unsettling voice glitching on the pager's small speaker. "So we get them out of the way. Now where does she live?"

"I'm sending the coordinates now." The whole kidnapping idea didn't sit right with Erik, but neither did sending a teenager down There in the first place. Besides, he _needed_ to get his hands on Aperture's legendary tech.

Erik took a deep breath before sending his boss the map, he would do whatever it took…

For Science.

—

It was the middle of the night, but Sophie couldn't sleep.

She had been thinking for a while, and had decided her parents deserved an apology. They were probably right about the dangerous equipment in that lab, and she had accidentally insulted her father's intelligence, the one thing she had always defended before. Besides, they still owed her an explanation.

As Sophie got out of bed, she realized something was _very_ wrong: the walls were scratched, the bedroom door was open, and her parents were nowhere to be found.

Panicking, Sophie ran through the house. She found no sign of her parents, but plenty of signs that a struggle had taken place. There was only one conclusion, her parents had been kidnapped.

*Ring* *Ring*, Sophie jumped 2 inches into the air before turning around and shakily picking up the phone. "Hello?"

" **Hello Miss Newell."**

"Advisor!" Sophie gasped as his modulated voice came through the speaker. So this was the "something else" he had come up with! "What have you done with my parents?"

" **Oh, they're safe. But if you ever want to see them again, you'll follow my instructions exactly."**

"W-what do you want?"

" **In the cookie jar in your kitchen, there is a flash drive and a map to Aperture Laboratories. Go to that location, and use the virus on the flash drive to shut down the Central AI. Tell no one what happened, or your parents will die."**

With that, he hung up. Sophie had no idea what a "Central AI" was, or how she would get to Aperture, but it didn't matter. All that mattered was that her parents were in danger, and it was all her fault.


	8. The Journey

Ellie woke up in a cold sweat. She didn't know how she knew, but she had learned to trust her gut on these things, and her gut told her Sophie was in danger.

Ellie quickly crept out of bed and ran to Sophie's house. The front door was open, increasing the likelihood that something was wrong. When she walked inside she was startled to find Sophie packing supplies. "What the heck are you doing?"

"My parents are being held for ransom." Sophie replied, still packing. "I'm going to pay it."

"Your parents are WHAT?! Hang on, I'll get dad."

"No!" Sophie yelled frantically. "He _knows where we are!_ If we get help, he'll _kill_ them!"

"Who is this guy?" Ellie was flabbergasted, why would anyone spy on Sophie's parents?

"He told me to call him "The Advisor". He works for this company called Pluot."

"Well what does he want?" Ellie began packing as well.

"None of your business!"

"It is my business because I'm coming with you!"

"No! This is my problem. I'm going alone."

"You sound just like your mother!"

"Is that a problem?.." There it was again. The ghost of a flare, the sense that her eyes should be _glowing_ with rage. "No, but she was always a loner too, until she met Wheatley. You don't have to be alone either."

"But this whole thing is _my fault._ What if you get hurt?" Sophie only dimly realized she had echoed her parents. "I could never forgive myself."

"And I could never forgive myself if _you_ got hurt!" Ellie paused. "Look Sophie. I don't know what it is, but you're special, I can feel it. We can't afford to lose you. Let me help."

Sophie sighed in resignation. "We'll need a car."

* * *

"This isn't going to work." Sophie said for the billionth time.

"Sure it will, he leaves the window down all the time!"

"Listen. I've heard a lot of terrible ideas, and you can trust me when I say this _is_ one. We can't just steal Aaron's car!"

"You have a better plan?"

"Fine, let's commit Grand Theft Auto."

After some careful maneuvering, and a lot of falling, they managed to climb through the window of Aaron's truck. Ellie was just wondering how they were going to start it when the engine sputtered to life. "Manual override." Sophie said proudly, holding two wires in her hands. "Dad taught me."

" Um...Ok. To the Northeast!"

"That has got to be the dumbest battle cry in history." And with that, they sped off into the night, leaving behind a very shocked Aaron.

 **Yeah, Wheatley probably would be good at hot-wiring a car. It fits in well with his "hacking" skills, and it could be one of the random memories he recovers occasionally.**


	9. The Breakout

"Rrrgh, come _on_. Ow!"

6 Hours. It had been 6 hours since Wheatley and Chell were dragged out of bed by three goons in masks and hauled to who knows where in the back of a truck. They had put up a fight of course (meaning Chell had put up a fight while Wheatley had scrambled for a weapon), but then they had brought out the tranquilizer darts. The only reason Wheatley knew how long they'd been out was because of his brand new decades old watch, and as for location, they definitely weren't in Eaden anymore.

" _Hey, isn't that from a movie? No. Focus, Wheatley, focus."_

" _Hurry_ Wheatley, these are the guys who called Sophie! She's probably There right now!

"I'm trying! This is way harder than it looks in the movies!"

Once upon a time, Wheatley might have let Chell do the work, or tried to get out of this rescue attempt altogether. But he had grown since then, and as soon as he woke up in this broom closet, he had broken his (expensive) glasses and started sawing through their rope bindings with the sharpest shard he could find.

"What's going on in there?"

" _Oh crap"_

As the guard burst through the door, Chell managed to surprise Wheatley yet again by grabbing the man's gun and braining him with it. "Come on."

"But we're still tied together!"

" _Come on!"_

"Ok, ok!" Wheatley barely had time to register how hot this was before they were off. Chell on his back firing warning shots everywhere and Wheatley trying awkwardly to punch anyone who came too close.

"Hey, I know we're a little busy with the whole "escaping" thing, but how are we going to get to Sophie? Is there some sort of truck we could borrow or- Look out!" Wheatley cut himself off as five guards appeared around the corner, forcing him to duck into the nearest door and slam the lock button.

Wait, what kind of door had a lock button?

Wheatley gasped as he found himself in a room full of incredible technology, the kind he hadn't seen since Aperture. A metal sign on the wall said "Pluot R&D Department". And in the center of the room was a machine Wheatley recognized from a documentary as a teleporter . "Look, our way out! Gimme those coordinates."

Being human, Wheatley no longer had a Cognitive Rerouter, but some might have attributed his decision to his natural "Wheatleyness". In reality, he was simply desperate to save his daughter. And Chell, loving Sophie just as much as he did, didn't argue as he pressed the button.

But accidentally setting the destination Z value to -9000? That was classic Wheatley.

"Ugh… Where are we?"

" _Welcome gentlemen to Aperture Science. Astronauts, War Heroes, Olympians, you're here because we want the best, and you are it. So, who's ready to make some science?_

 **Haha! Wheatley, meet Karma. Karma, I'm sure you know Wheatley. You two are going to have a** _ **lot**_ **of fun together.**


	10. The Lab

"This is it?"

When Sophie heard the words "underground research facility", she, like most people, thought of an impressive, futuristic entrance- or at least a parking lot. So when she and Ellie drove 12 miles only to find an old shed, she was understandably confused.

"This is the only man-made thing for miles. He did say it was underground. Maybe this is an emergency elevator or something."

"More likely the Advisor sent us a bad map." Sophie grumbled. "Even if there was an elevator in there, there's no way it could still be-"

 _Woosh! Clank. Hiss..._

 _*sigh*_ "Working."

* * *

GLaDOS had noticed the Companion Cube's signal, of course. She could feel any piece of Aperture tech in a fifty mile radius. But she had sworn off anything to do with the Lunatic or the Moron 14 years ago, and she felt no curiosty about them or their (shudder), _feelings_ for each other. That didn't mean she hadn't taken precautions though. Precautions like rerouting the escape elevator to lead directly to the test chambers to slow intruders down. And if she got some valuable Science out of an attempted break-in, well that was what she called fate.

 **"Hello. And again, welcome to the Aperture Science Computer Aided Enrichment Center..."**


	11. The Tests

" **Hello. And again, welcome to the Aperture Science Computer Aided Enrichment Center. I can see there are two of you, so I've prepped the co-op course. You will find the necessary equipment in the entrance room."**

Sophie and Ellie stepped out of the elevator into a glass cell. There was a small, podlike bed, a radio, and two pairs of sleek white boots. **"These are Aperture Science Long Fall Boots, they will nullify any fall damage you may or may not receive over the course of testing. Make no attempt to test without them."**

Sophie didn't understand how these boots could protect you from falling, but any skepticism she had was blown out the window with what happened next.

 **"The portal will open in three, two, one."**

A shimmering blue hole opened on the white wall behind her, showing a view of the room outside their cell. When Sophie looked through the glass, she could see an identical orange hole opening into her cell. Her first thought was: _"Is that really what I look like from the back?"_ But her second thought was _"Holy Freeman, just like in the story!"_

* * *

 _"Now this lady, she had a magic bow. First off, it never ran out of arrows. But what really made it special was what happened when you shot it! It could create magic tunnels between any two places you hit. You could walk through one magical space-hole and come out the other, just like you were walking through a door!_

 _"Can I have a magic bow daddy?"_

 _"Um... they only made the one, and this kingdom is very far away. Plus there's the fact that this is all just make-believe. So... no._

* * *

Evidently, Wheatley had based his bedtime stories on this "Enrichment Center". But that would mean that the evil queen from the story was this voice. The "Her" Sophie's parents had mentioned. _The Central AI._

 _"Fine."_ Sophie decided. This thing wanted tests? Sophie would test. But she would be on her toes from now on, because she had a job to do, and her parents were counting on her to do it right.

 _"Look out lady, I'm coming for you."_

* * *

" _Alright, let's get started. This first test involves something the lab boys call 'repulsion gel'.'_ _You're not part of the control group, by the way. You get the gel. Last poor son of a gun got blue paint!"_

Wheatley tuned out the restof the recording. He and Chell had quickly figured out they were in "Old Aperture," AKA What-was-at-the-bottom-of that-pit-and-apparently-he-hadn't-finished-his-payback-yet...place. The good news was: Chell knew a way out, the bad news: _She_ had probably sealed it off. To make matters worse, they had no portal gun, no boots, no _anything_ except for this rope that they had finally gotten free of. Hence why they were currently trying to make a grappling hook.

"Are you sure this is going to work? You're not bloody Batman!"

"It has to work." Chell replied, still fiddling with the rope. "If we can find the equipment closet, there should be a prototype portal gun."

"Do you know where the equipment closet is?"

"Not a clue." Chell replied, picking up her new makeshift grappling hook. "But since when has anything been easy for us?"


	12. The Positive

It wasn't until test 10 that GLaDOS began to worry.

Subject 84720, "Ellie", was nothing special, save for her uncanny ability to dodge turrets. But Subject 8184, "Sophie", was a different story. First she portaled a cube directly onto a button, a move GLaDOS had only seen one other subject do.

Then, Sophie had started destroying all the secruity cameras, revealing just how much she looked like the Lunatic, and prompting GLaDOS to run a DNA test on her hair.

GLaDOS, being an incredibly rational and mature supercomputer, definitely didn't panic when the results came back positive. Sophie was Chell's daughter, and would thus have to be disposed of immdiately, a simple gas chamber would do the trick. Of course, that raised the question of the girl's father-

 _Oh_

Suddenly, GLaDOS wished she had the ability to throw up.


	13. The Escape

For as long as Ellie could remember, she had been different. She was soft-spoken, socially awkward, and had an irrational attachment to her plush vortigaunt (She had kept it until she was 8). But the strangest thing about Ellie was her premonitions.

Almost as soon as she had been born, Ellie had noticed things that others didn't, made connections that others hadn't considered, _seen_ things that most people were blind to. Sometimes she would have dreams, and sometimes she would draw odd pictures, but most of the time it was just a feeling, a vague sense that something bad was about to happen. She had gotten that feeling the night of the dance in her family's field, and she was feeling it again now.

" **Congratulations on solving the last test. Please wait in this extra chamber for your reward."**

The computerized voice darkened. **"Your** _ **final**_ **reward…"**

" _Neurotoxin Emitters Online."_

"It's a trap!"

Thinking quickly, Ellie used the brace on her boot to pry off a wall panel, allowing Sophie access to the vacuum tube from the last test. She placed a portal under the tube and one on the wall, sucking up the neurotoxin. Then Ellie flung a cube at the small vent, crushing it completely.

" **Fine, I prefer to save that for special occasions anyway. Deploying a much less expensive trap now."**

" _Hello?"_

" _I see you…"_

Sophie momentarily panicked before her Mother's DNA kicked in. She tricked one of the turrets into firing at the observation window, then portalled up into the room and ran out the door, Ellie close behind.

* * *

"We found it!"

It had been slow going, _very_ slow, but Wheatley and Chell had finally found the entrance to the test track. From there, it was a simple matter to find the equipment room and "manually override" the lock. Inside, they found rows of primitive portal devices, cans of spare gel, and, dumped on a table as if someone had forgotten it, a jar of tiny metallic grains labelled "Aperture Science Human Improvement Nanites."

"Perfect! We can ask for directions!" Wheatley walked over to the jar and cleared his throat: "Right, nanobots. I can't hear you anymore, so we're gonna have to do-I don't know, charades or something. Now, do you by chance know a way out of this scrap heap?"

The nanobots quickly rearranged themselves into words, and Wheatley responded cordially. "Oh sure, No problem!"

The nanobots shifted again, and Wheatley scribbled something on a piece of paper before walking back over to Chell. "There's our exit."

Chell nodded tersely and began packing their supplies, but stopped when she saw Wheatley picking up the jar of nanobots. "What are you doing?"

"Oh..." Wheatley said sheepishly, "I, uh, kinda promised to take them with us. I'm just gonna let them go in the Enrichment Center, no problem at all."

"Fine," Chell said, stuffing cans of conversion gel into her pockets, "but you're carrying them."


	14. The Revelation

"Is this it?" Sophie asked. They were standing in some sort of server room. The words: "Central Core uplink ready" flashed on a giant screen, and a USB port was ready on the console.

"Seems like as good a place as any." Ellie replied, holding the Pluot thumb drive. "Lets plug this thing in, so this crazy computer will never be a threat to anyone again."

But before they could do anything, the lights and screen blinked off, and two robots stepped through a portal on the wall.

" **I honestly, truly, didn't think you'd fall for that."**

* * *

The Fact Sphere didn't get bored. He was the greatest collection of knowledge in the known universe, there was no room in his hard drive for silly emotions like boredom _._ But if he _did_ have the ability to feel bored, he thought he would be bored right now.

He had been in this room for years, monitoring the contents of these neurotoxin tubes and ensuring that they didn't fall to nonlethal levels. He suspected that _She_ was just keeping him busy, but who was he to argue with the Central AI? Still, the fact remained that these two humans were the most interesting thing he'd seen all day.

Wait, what?

"Hey, Fact Sphere! Long time no see!"

The Fact Sphere sighed. "Hello moron."

"I am NOT a-ugh. How'd you know it was me?"

"Only one voice in the universe is that nerve-grating."

"Well _thank you_." Wheatley replied sarcastically "Look, have you seen a little girl, looks like Chell, but with blue eyes?"

The Fact Sphere wasn't programmed to lie, but it couldn't tell the moron that GLaDOS had taken this girl prisoner, so he settled for a compromise: "You are not authorized to know the girl's location. Your presence will be reported to the Central AI, and-"

The Fact Sphere never got a chance to finish his sentence, since Chell violently pulled him off his rail and glared at him with an intensity Wheatley had never seen before. _"_ _Where is she!?"_

The Fact Sphere produced a simulated gulp. He _definitely_ wasn't programmed for this.

* * *

 **"Hello again lunatic jr. Congratulations on being captured even faster than your mother was."**

The robots had dragged Sophie and Ellie into a huge chamber, then hauled Sophie in front of several turrets. The voice seemed louder here, and when Sophie looked up, she realized why. _She_ was right there.

A massive conglomeration of wires and metal and heaven knew what else hung from the ceiling. The massive body attached to a sleek white head, whose malevolent eye was glaring at Sophie with all the intimidation it could muster. Stamped on one of the monstrosity's discs was a faded label: GLaDOS.

 **"A peer review has found you unfit for testing."** She-GLaDOS,-said. **"It's not your fault, it's just in your DNA"**

"What is?!" Sophie demanded. "What have you got against my family?"

 **"Your mother was a deranged psychopath who nearly destroyed me."** GLaDOS replied, as screens folded out from behind the panels. **"And your father-well, see for yourself."**

With that, the screens lit up, and the words Ellie had heard over and over in her nightmares boomed from the speakers.

 _"I am NOT. a. moron!"_

* * *

Sophie was stunned. How could this robot be her father? How could he be in GLaDOS' body? But as impossible as it was, there was no mistaking that voice, and Sophie watched with growing horror as Wheatley went from yelling at Chell, to testing her, to- no... _N_ _o!_

Ellie was no less horrified by the recording (actually, Sophie probably had it worse. That _thing_ was her father), but she had the presence of mind to remember their mission. She wrestled away from the robot's grip, sprinted over to a computer, and jabbed the thumb drive into it's USB port.

GLaDOS screamed in pain, and the panels covering the walls jerked violently. One slid aside to reveal a glass tube, with promptly spat out the unlikely couple of the hour: Sophie's parents.

* * *

Wheatley tumbled out of the tube and immediately noticed something was wrong. Sophie was staring at a screen, its' feed frozen on an image of his worst moment: _That part._

Wheatley reached for his daughter, but she flinched away, tears in her eyes. "How could you?"

"Sophie, please. Let me explain-"

"No! Get away from m-"

Sophie never got the chance to finish her sentence. At that moment, a green dart hit her neck, and she collapsed, an expression of fear frozen on her face.

* * *

Wheatley screamed as his daughter fell. "What was that? Who shot her?"

 **"That was a powerful nerve agent made in this very facility."** Came a deep, garbled voice from behind them. **"As for who I am, most people know me as the advisor, but you can call me Wallace Breen."**


	15. The End

"Wallace Breen?" Wheatley was devastated, and as many people do in times of high emotion, he said something stupid: "But you're dead!"

" **I would be,"** Came Breen's voice, **"if I hadn't accepted the Combine's offer like an idiot! If I hadn't become…this."** With that he stepped into the light, revealing that he was no longer a man, but instead resembled some sort of giant grub in a wheelchair. Tubes and wires snaked around his emaciated body, and his face -if you could call it a face- was covered by a Bane-like mask. **"I searched for this place for years, hoping to find a way to be human again. But now I can do better, With this tech, I could live for centuries! Search the lab!"**

 _"Oh, is t-that all you want?"_

Everyone in the room jumped as _her_ voice crackled over the speakers, " _You can sabotage me, you can run from me, you can even shut me down, but you will_ never _take this facility, even if I die. Cave Johnson's legacy_ will _be protected."_ GLaDOS said that last sentence with such conviction, Wheatley almost heard humanity in her voice, and he wondered dimly what would happen to Caroline when this was over.

Four claws erupted from the walls, dragging Breen and his associates into the depths of the facility. _"You wanted to be immortal? Fine, enjoy your eternal life as root vegetables. As for you, moron, I would suggest leaving while you still can. This place won't last long without me."_

 **"How?!"** Breen screamed as he was hauled away. **"How can it still be functional?"**

 _"I'm not an it."_ GLaDOS growled, a spark leaping from her head. _"I'm a her."_

With that, the door slammed shut, the lights went out, and GLaDOS went limp, leaving Chell, Wheatley, Ellie, and Sophie alone in the room. "Central Core offline," said the announcer, "manual shutdown commencing."

The escape elevator came down, but it was too late. Even if they could get Sophie home anytime soon, Wheatley doubted that Dr. Dillon had a cure for neurotoxin. Their daughter was as good as dead.

 _Unless..._

Wheatley hesitantly brought out the nanobots, and Chell wordlessly gave her consent. Together, they awkwardly poured the nanites on Sophie's wounds and into her mouth, then carried her gently into the elevator.

* * *

After aliens from another dimension invaded the planet, humanity had pretty much seen it all. So the townspeople were more relived than surprised when Wheatley once again stumbled into Eaden. And they were more than happy to gather their shovels and picks and help seal off that accursed lab once and for all.

Wheatley snickered when the news came in that Pluot CEO Johnathan Coulton had gone missing, knowing full well the man was currently inhabiting a potato, and probably in lunar orbit. And while Sophie was understandably nervous when she woke up, she, like her mother, gave Wheatley a second chance.

"So, how did you guys really fall in love?"

"That's a long story sweetie." Wheatley replied, smiling. "A story about meteors, signals, apologies, and that tricky little thing called humanity..."

 **The End.**


	16. Epilogue

" _If you're interested in an additional sixty dollars, flag down a test associate and let 'em know. You could walk out of here with a hundred and twenty weighing down your bindle if you let us take you apart, put some science stuff in you, then put you back together good as new._ "

Sophie tossed and turned in her bed. She could feel something-actually, a _lot_ of somethings crawling under her skin and through her veins. They dug into her bones, twisted her muscles, and remodeled her into a being that could only be possible where the impossible was easy.

" **You saw what your father was…"** GLaDOS said, her cruel voice haunting Sophie's dreams, just as it did her mother's. **"What does that make you?"**

Sophie woke with a scream, her gut searing with pain, and her eyes glowing bright blue.

 **Ok, disclaimer time:**

 **I did not come up with the name Sophie, it came from a Blue Sky story over on AO3 called "Ready or Not". My Sophie looks different, but that's where I got the name.**

 **The name Pluot comes from "Portal 3", a hilarious Portal comic from DeviantArt, it's not very kid friendly though.**

 **The idea of Breen becoming an Advisor Grub came from a joke story by one of Valve's writers, it's probably the closest thing we'll ever have to Half Life 3.**

 **Last but not least, Blue Sky is owned by Wafflestories.**

 **724 Out.**


End file.
